The landscape of cytokinin binding by a plant nodulin

Nodulation is an extraordinary symbiotic interaction between leguminous plants and nitrogen‐fixing bacteria (rhizobia) that assimilate atmospheric nitrogen (in root nodules) and convert it into compounds suitable for the plant host. A class of plant hormones called cytokinins are involved in the nodulation process. In the model legume Medicago truncatula , nodulin 13 (MtN13), which belongs to the pathogenesis‐related proteins of class 10 (PR‐10), is expressed in the outer cortex of the nodules. In general, PR‐10 proteins are small and monomeric and have a characteristic fold with an internal hydrophobic cavity formed between a seven‐stranded antiparallel β‐sheet and a C‐terminal α‐helix. Previously, some PR‐10 proteins not related to nodulation were found to bind cytokinins such as trans ‐zeatin. Here, four crystal structures of the MtN13 protein are reported in complexes with several cytokinins, namely trans ‐zeatin, N 6 ‐isopentenyladenine, kinetin and N 6 ‐benzyladenine. All four phytohormones are bound in the hydrophobic cavity in the same manner and have excellent definition in the electron‐density maps. The binding of the cytokinins appears to be strong and specific and is reinforced by several hydrogen bonds. Although the binding stoichiometry is 1:1, the complex is actually dimeric, with a cytokinin molecule bound in each subunit. The ligand‐binding site in each cavity is formed with the participation of a loop element from the other subunit, which plugs the only entrance to the cavity. Interestingly, a homodimer of MtN13 is also formed in solution, as confirmed by small‐angle X‐ray scattering (SAXS).